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Mini-Workshop "BioData Visualization & Subcellular Localization"

In this workshop, we are going to discuss the methods and tools that help life scientists exploit the large biological datasets to gain insight into underlying biological and biomedical mechanical processes by using data visualization, networking analysis and protein subcellular localization.

Organizers: Lu Zhu , Björn Sommer

Place:

Bielefeld University, U10-146

Date:

Feburay 26th, 2015

Guests

Name

Institution

City

Country

William Duddy

Center for Research in Myology

Paris

France

Thorben Wallmeyer

Arvato AG

Gütersloh

Germany

Jens Krüger

Applied Bioinformatics Group,University of Tübingen

Tübingen

Germany

Sabine Müller

Saarland University

Saarbrücken

Germany

Timetable

Time

Speaker

Topic

14h

William Duddy

Interactomics and subcellular localizations

14h30

Bjoern Sommer

Subcellular Localization Prediction and Visualization with CmPI

15h

Sabine Müller

Non-synonymous single nucleotide variants and pathogenicity

15h30

Coffee Break

16h

Thorben Wallmeyer

Extending Frametex scope from network reconstruction to localization

16h30

Lu Zhu

Network–based localization prediction approaches

17h

Jens Krueger

MoSGrid – A Science Gateway for Molecular Simulations

17h30

Free discussion

19h30

Dinner

Abstracts

Jens Krüger : MoSGrid – A Science Gateway for Molecular Simulations

The MoSGrid portal offers a platform for high-quality molecular simulations on distributed compute infrastructures for scientists with all kinds of background and experience levels [1]. A user-friendly interface enables the ease-of-use of modern chemical simulation protocols well established in the field. The usage of carefully curated workflows annotated with metadata largely improves the reproducibility of simulations in the sense of good lab practice. MoSGrid supports applications from the domains of quantum chemistry (QC), molecular dynamics (MD), and protein-ligand docking. The talk will give insight to features of MoSGrid, inform about recent developments and highlight ongoing collaborations with XSEDE via MoSGrid US.

Lu Zhu : Network–based localization prediction approaches

Here we will discusses the existing methods and tools of the SCL predictions, especially the methods based on protein-protein interaction networks; the advantages and the limits of these methods concerning the prediction performance, accuracy, the possibility of graphic display organized on subcellular localizations, etc. And a framework is proposed which should improve the existing methods and the graph display. It should allow user to localize all the proteins of query network in short-time as well as with less complexity.

The CELLmicrocosmos 4 PathwayIntegration (CmPI) is a tool which was developed to combine the mesoscopic and functional level. The mesoscopic level, representing cell components and their sub structures, is visualized as a virtual cell environment with extensive exploration capabilities. At the functional level, originally only metabolic pathways from KEGG were localized by using information from various databases included in DAWIS-M.D.

CmPI was extended in the recent years to also cover protein-protein interaction networks and gene-related data. This data can be imported via various data formats, such as GraphML or SBML.

The potential localizations results from the databases often contain multiple entries for a single biological instance. To explore and analyze this data, the Subcellular Localization Charts were introduced. Different chart categories are available to explore the localization data. For example, the Co-localization charts compute a value for all selected biological instances based on the localization entries of their nearest neighbors. Moreover, the 2D Network visualization was extended in order to combine the normalized number of localization entries with the network structure representation. Therefore, the process of localization prediction is strongly improved now.

The future aim is to develop localization prediction algorithms in the dissertation project of Lu Zhu in the context of the DFG Research Training Group Computational Methods for the Analysis of the Diversity and Dynamics of Genomes (DiDy). These algorithms will automatize the localization process while maintaining the visual evaluation capabilities of CmPI. Therefore, a Node Placing Algorithm plugin interface was implemented, based on the internally well-established technology of the CELLmicrocosmos 2 MembraneEditor.

How to reach the Workshop place

The workshop takes place on the 10th floor of the building U, where the DiDy Research Group is situated.

By train: Arriving at Bielefeld Hbf (main station), exit the building towards the city center; you should see the Bielefelder Hof hotel in front of you (if you see a Cinemaxx, you are on the wrong side!). Cross the street to get to the underground tram (Stadtbahn / U-Bahn) station. Take tram number 4 towards Universität / Lohmannshof. Exit the tram at Universität. Walk up the stairs and cross the red bridge towards the university main building. Enter it and walk up the stairs. You are now standing in the main hall. Turn right, walk about 50m, and look on your left hand side for a staircase labelled U,V,M. Take the elevator to the 10th floor (if the elevator does not go up to the 10th floor, you are at the wrong elevator!). When exiting, turn left and again left. You are now in U10, where our offices are.